SOLiDzipper: A High Speed Encoding Method for the Next-Generation Sequencing Data

Background Next-generation sequencing (NGS) methods pose computational challenges of handling large volumes of data. Although cloud computing offers a potential solution to these challenges, transferring a large data set across the internet is the biggest obstacle, which may be overcome by efficient encoding methods. When encoding is used to facilitate data transfer to the cloud, the time factor is equally as important as the encoding efficiency. Moreover, to take advantage of parallel processing in cloud computing, a parallel technique to decode and split compressed data in the cloud is essential. Hence in this review, we present SOLiDzipper, a new encoding method for NGS data. Methods The basic strategy of SOLiDzipper is to divide and encode. NGS data files contain both the sequence and non-sequence information whose encoding efficiencies are different. In SOLiDzipper, encoded data are stored in binary data block that does not contain the characteristic information of a specific sequence platform, which means that data can be decoded according to a desired platform even in cases of Illumina, Solexa or Roche 454 data. Results The main calculation time using Crossbow was 173 minutes when 40 EC2 nodes were involved. In that case, an analysis preparation time of 464 minutes is required to encode data in the latest DNA compression method like G-SQZ and transmit it on a 183 Mbit/s bandwidth. However, it takes 194 minutes to encode and transmit data with SOLiDzipper under the same bandwidth conditions. These results indicate that the entire processing time can be reduced according to the encoding methods used, under the same network bandwidth conditions. Considering the limited network bandwidth, high-speed, high-efficiency encoding methods such as SOLiDzipper can make a significant contribution to higher productivity in labs seeking to take advantage of the cloud as an alternative to local computing. Availability http://szipper.dinfree.com . Academic/non-profit: Binary available for direct download at no cost. For-profit: Submit request for for-profit license from the web-site

Structural performance experiment by moving cart to mount measurement sensors

The development of a measurement system for the purpose of structural performance evaluation has been needed. This work introduces a moving cart system on which to mount measurement sensors to measure acceleration and sound pressure in the time domain and an impact hammer for external excitation. The measurement data are utilized to evaluate the structural performance based on a mixed approach to directly and indirectly collect response data by a microphone and an accelerometer, respectively. The reliability of the measurement data is improved by the utilization of multiple sensors. The structural state is investigated by the power spectral density estimate (PSE) or proper orthogonal mode (POM) of the sound pressure and acceleration data. The applicability of the system is illustrated in a field test

An Exploratory Pilot Study with Plasma Protein Signatures Associated with Response of Patients with Depression to Antidepressant Treatment for 10 Weeks.

Major depressive disorder (MDD) is a leading cause of global disability with a chronic and recurrent course. Recognition of biological markers that could predict and monitor response to drug treatment could personalize clinical decision-making, minimize unnecessary drug exposure, and achieve better outcomes. Four longitudinal plasma samples were collected from each of ten patients with MDD treated with antidepressants for 10 weeks. Plasma proteins were analyzed qualitatively and quantitatively with a nanoflow LC-MS/MS technique. Of 1153 proteins identified in the 40 longitudinal plasma samples, 37 proteins were significantly associated with response/time and clustered into six according to time and response by the linear mixed model. Among them, three early-drug response markers (PHOX2B, SH3BGRL3, and YWHAE) detectable within one week were verified by liquid chromatography-multiple reaction monitoring/mass spectrometry (LC-MRM/MS) in the well-controlled 24 patients. In addition, 11 proteins correlated significantly with two or more psychiatric measurement indices. This pilot study might be useful in finding protein marker candidates that can monitor response to antidepressant treatment during follow-up visits within 10 weeks after the baseline visit

Dihydrotestosterone-Inducible IL-6 Inhibits Elongation of Human Hair Shafts by Suppressing Matrix Cell Proliferation and Promotes Regression of Hair Follicles in Mice

Autocrine and paracrine factors are produced by balding dermal papilla (DP) cells following dihydrotestosterone (DHT)-driven alterations and are believed to be key factors involved in male pattern baldness. Herein we report that the IL-6 is upregulated in balding DP cells compared with non-balding DP cells. IL-6 was upregulated 3hours after 10–100nM DHT treatment, and ELISA showed that IL-6 was secreted from balding DP cells in response to DHT. IL-6 receptor (IL-6R) and glycoprotein 130 (gp130) were expressed in follicular keratinocytes, including matrix cells. Recombinant human IL-6 (rhIL-6) inhibited hair shaft elongation and suppressed proliferation of matrix cells in cultured human hair follicles. Moreover, rhIL-6 injection into the hypodermis of mice during anagen caused premature onset of catagen. Taken together, our data strongly suggest that DHT-inducible IL-6 inhibits hair growth as a paracrine mediator from the DP

Primary malignant melanoma of the vagina in a postmenopausal woman

Primary malignant melanoma of the vagina, a very rare malignancy, is very aggressive and highly metastatic. Primary vaginal melanoma usually has a poor clinical prognosis, because it is often diagnosed at an advanced stage. We present a case of an 80-year-old postmenopausal woman with pigmented lesion of the vagina. The histopathology of the lesion revealed malignant melanoma. The patient was treated surgically, with wide local excision of the vaginal lesion. Left inguinal lymphadenectomy, based on the positron emission tomography-computed tomography (PET-CT) images, found metastatic melanoma. We present a case report of postmenopausal woman with primary vaginal melanoma

The intratumoral administration of ferucarbotran conjugated with doxorubicin improved therapeutic effect by magnetic hyperthermia combined with pharmacotherapy in a hepatocellular carcinoma model

BACKGROUND: Local hyperthermia of tumor in conjunction with chemotherapy is a promising strategy for cancer treatment. The aim of this study was to evaluate the efficacy of intratumoral delivery of clinically approved magnetic nanoparticles (MNPs) conjugated with doxorubicin to simultaneously induce magnetic hyperthermia and drug delivery in a hepatocellular carcinoma (HCC) model. MATERIALS AND METHODS: HCC cells expressing luciferase were implanted into the flank of BALB/c-nu mice (n = 19). When the tumor diameter reached 7–8 mm, the animals were divided into four groups according to the injected agents: group A (normal saline, n = 4), group B (doxorubicin, n = 5), group C (MNP, n = 5), and group D (MNP/doxorubicin complex, n = 5). Animals were exposed to an alternating magnetic field (AMF) to receive magnetic hyperthermia, and intratumoral temperature changes were measured. Bioluminescence imagings (BLIs) were performed before treatment and at 3, 7, and 14 days after treatment to measure the tumoral activities. The relative signal intensity (RSI) of each tumor was calculated by dividing the BLI signal at each time point by the value measured before treatment. At day 14 post-treatment, all tumor tissues were harvested to assess the apoptosis rates by pathological examination. RESULTS: The rise in temperature of the tumors was 1.88 ± 0.21°C in group A, 0.96 ± 1.05°C in B, 7.93 ± 1.99°C in C, and 8.95 ± 1.31°C in D. The RSI of the tumors at day 14 post-treatment was significantly lower in group D (0.31 ± 0.20) than in group A (2.23 ± 1.14), B (0.94 ± 0.47), and C (1.02 ± 0.21). The apoptosis rates of the tumors were 11.52 ± 3.10% in group A, 23.0 ± 7.68% in B, 25.4 ± 3.36% in C, and 39.0 ± 13.2% in D, respectively. CONCLUSIONS: The intratumoral injection of ferucarbotran conjugated with doxorubicin shows an improved therapeutic effect compared with doxorubicin or ferucarbotran alone when the complex is injected into HCC tissues exposed to AMF for magnetic hyperthermia. This strategy of combining doxorubicin and MNP-induced magnetic hyperthermia exhibits a synergic effect on inhibiting tumor growth in an HCC model